build(deps): update Quarkus to 3.8 LTS (#609)

* build(deps): update Quarkus to 3.8 LTS * add hibernate format mapper override * remove no longer necessary lazy init * disable openapi management / swagger UI unless in dev mode * remove duplicate healthcheck override * reduce healthcheck start periods * correct healthcheck URL * use authproxy image which contains wget for healthcheck * correct healthchecks for vertx agent test applications
cryostatio · Sep 30, 2024 · 739a65f · 739a65f
1 parent 2e86562
commit 739a65f
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Showing 31 changed files with 176 additions and 184 deletions.
diff --git a/compose/auth_proxy.yml b/compose/auth_proxy.yml
@@ -12,12 +12,6 @@ services:
       QUARKUS_HTTP_PROXY_ENABLE_FORWARDED_PREFIX: "true"
       QUARKUS_HTTP_ACCESS_LOG_PATTERN: long
       QUARKUS_HTTP_ACCESS_LOG_ENABLED: "true"
-    healthcheck:
-      test: curl --fail http://cryostat:8181/health/liveness || exit 1
-      interval: 10s
-      retries: 3
-      start_period: 30s
-      timeout: 5s
   auth:
     # the proxy does not actually depend on cryostat being up, but we use this
     # to ensure that when the smoketest tries to open the auth login page in a
@@ -31,7 +25,7 @@ services:
         limits:
           cpus: "0.1"
           memory: 32m
-    image: ${OAUTH2_PROXY_IMAGE:-quay.io/oauth2-proxy/oauth2-proxy:latest}
+    image: ${OAUTH2_PROXY_IMAGE:-quay.io/oauth2-proxy/oauth2-proxy:latest-alpine}
     command:
       - --alpha-config=/tmp/auth_proxy_alpha_config.yml
     volumes:
@@ -49,10 +43,10 @@ services:
       CRYOSTAT_PROXY_PORT: ${CRYOSTAT_PROXY_PORT}
     restart: unless-stopped
     healthcheck:
-      test: wget -q --spider ${CRYOSTAT_PROXY_PROTOCOL}://localhost:${CRYOSTAT_PROXY_PORT}/ping || exit 1
+      test: wget --no-check-certificate -q --spider ${CRYOSTAT_PROXY_PROTOCOL}://localhost:${CRYOSTAT_PROXY_PORT}/ping || exit 1
       interval: 10s
       retries: 3
-      start_period: 30s
+      start_period: 10s
       timeout: 5s
 
 volumes:

diff --git a/compose/cryostat-grafana.yml b/compose/cryostat-grafana.yml
@@ -26,5 +26,5 @@ services:
       test: curl --fail http://localhost:3000/ || exit 1
       retries: 3
       interval: 30s
-      start_period: 30s
+      start_period: 10s
       timeout: 1s
diff --git a/compose/cryostat.yml b/compose/cryostat.yml
@@ -36,12 +36,14 @@ services:
         -Dcom.sun.management.jmxremote.ssl=false
         -Dcom.sun.management.jmxremote.local.only=false
     restart: unless-stopped
-    healthcheck:
-      test: curl --fail http://cryostat:${CRYOSTAT_HTTP_PORT}/health/liveness || exit 1
-      interval: 10s
-      retries: 3
-      start_period: 30s
-      timeout: 5s
+    # FIXME reenable this check. Somehow after upgrading to Quarkus 3.8, this check fails with 'connection refused',
+    # but the container comes up successfully without it and shelling into the container later to run curl succeeds
+    # healthcheck:
+    #   test: curl --fail http://cryostat:${CRYOSTAT_HTTP_PORT}/health/liveness || exit 1
+    #   interval: 10s
+    #   retries: 3
+    #   start_period: 30s
+    #   timeout: 5s
 
 volumes:
   jmxtls_cfg:

diff --git a/compose/db.yml b/compose/db.yml
@@ -27,7 +27,7 @@ services:
       test: pg_isready -U cryostat -d cryostat || exit 1
       interval: 10s
       retries: 3
-      start_period: 30s
+      start_period: 10s
       timeout: 5s
 
 volumes:

diff --git a/compose/jfr-datasource.yml b/compose/jfr-datasource.yml
@@ -29,8 +29,8 @@ services:
         -Dcom.sun.management.jmxremote.ssl=false
         -Dcom.sun.management.jmxremote.local.only=false
     healthcheck:
-      test: curl --fail ${CRYOSTAT_PROXY_PROTOCOL}://localhost:${CRYOSTAT_PROXY_PORT}/ || exit 1
+      test: curl --fail http://localhost:8080/ || exit 1
       retries: 3
       interval: 30s
-      start_period: 30s
+      start_period: 10s
       timeout: 1s
diff --git a/compose/sample_apps/vertx-cryostat-agent.yml b/compose/sample_apps/vertx-cryostat-agent.yml
@@ -63,7 +63,7 @@ services:
       - "8911"
     restart: always
     healthcheck:
-      test: curl --fail http://localhost:8081 || exit 1
+      test: curl --fail http://localhost:8082 || exit 1
       interval: 10s
       retries: 3
       start_period: 30s
@@ -102,7 +102,7 @@ services:
       - "8912"
     restart: always
     healthcheck:
-      test: curl --fail http://localhost:8081 || exit 1
+      test: curl --fail http://localhost:8083 || exit 1
       interval: 10s
       retries: 3
       start_period: 30s
@@ -126,7 +126,7 @@ services:
       - "8084:8084"
     restart: always
     healthcheck:
-      test: curl --fail http://localhost:8081 || exit 1
+      test: curl --fail http://localhost:8084 || exit 1
       interval: 10s
       retries: 3
       start_period: 30s

diff --git a/pom.xml b/pom.xml
@@ -35,21 +35,17 @@
     <io.cryostat.core.version>4.0.0-SNAPSHOT</io.cryostat.core.version>
     <org.openjdk.jmc.version>9.0.0</org.openjdk.jmc.version>
 
-    <org.apache.commons.codec.version>1.16.1</org.apache.commons.codec.version>
     <org.apache.commons.io.version>2.16.1</org.apache.commons.io.version>
     <org.apache.commons.collections.version>4.4</org.apache.commons.collections.version>
-    <org.apache.httpcomponents.version>5.2.1</org.apache.httpcomponents.version>
-    <org.apache.commons.lang3.version>3.14.0</org.apache.commons.lang3.version>
     <org.apache.commons.validator.version>1.8.0</org.apache.commons.validator.version>
     <org.projectnessie.cel.bom.version>0.4.4</org.projectnessie.cel.bom.version>
     <com.google.protobuf-java.version>3.25.2</com.google.protobuf-java.version>
     <com.nimbusds.jose.jwt.version>9.41.1</com.nimbusds.jose.jwt.version>
     <org.testcontainers.bom.version>1.20.1</org.testcontainers.bom.version>
     <quarkus.platform.artifact-id>quarkus-bom</quarkus.platform.artifact-id>
     <quarkus.platform.group-id>io.quarkus.platform</quarkus.platform.group-id>
-    <quarkus.platform.version>3.2.12.Final</quarkus.platform.version>
-    <quarkus-quinoa.version>2.2.5</quarkus-quinoa.version>
-    <io.netty.version>4.1.108.Final</io.netty.version>
+    <quarkus.platform.version>3.8.6</quarkus.platform.version>
+    <quarkus-quinoa.version>2.3.10</quarkus-quinoa.version>
     <org.codehaus.mojo.build.helper.plugin.version>3.6.0</org.codehaus.mojo.build.helper.plugin.version>
     <org.codehaus.mojo.exec.plugin.version>3.4.1</org.codehaus.mojo.exec.plugin.version>
     <assembly-plugin.version>3.7.1</assembly-plugin.version>
@@ -60,19 +56,12 @@
     <com.google.java-format.version>1.23.0</com.google.java-format.version>
     <com.mycila.license.maven.plugin.version>4.6</com.mycila.license.maven.plugin.version>
     <surefire-plugin.version>3.5.0</surefire-plugin.version>
-    <surefire.rerunFailingTestsCount>2</surefire.rerunFailingTestsCount>
+    <surefire.rerunFailingTestsCount>0</surefire.rerunFailingTestsCount>
     <failsafe-plugin.version>3.5.0</failsafe-plugin.version>
     <failsafe.rerunFailingTestsCount>${surefire.rerunFailingTestsCount}</failsafe.rerunFailingTestsCount>
   </properties>
   <dependencyManagement>
     <dependencies>
-      <dependency>
-        <groupId>io.netty</groupId>
-        <artifactId>netty-bom</artifactId>
-        <version>${io.netty.version}</version>
-        <type>pom</type>
-        <scope>import</scope>
-      </dependency>
       <dependency>
         <groupId>${quarkus.platform.group-id}</groupId>
         <artifactId>${quarkus.platform.artifact-id}</artifactId>
@@ -161,6 +150,10 @@
       <groupId>io.quarkus</groupId>
       <artifactId>quarkus-vertx</artifactId>
     </dependency>
+    <dependency>
+      <groupId>io.quarkus</groupId>
+      <artifactId>quarkus-netty</artifactId>
+    </dependency>
     <dependency>
       <groupId>io.quarkus</groupId>
       <artifactId>quarkus-smallrye-openapi</artifactId>
@@ -225,12 +218,10 @@
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-lang3</artifactId>
-      <version>${org.apache.commons.lang3.version}</version>
     </dependency>
     <dependency>
       <groupId>commons-codec</groupId>
       <artifactId>commons-codec</artifactId>
-      <version>${org.apache.commons.codec.version}</version>
     </dependency>
     <dependency>
       <groupId>commons-io</groupId>
@@ -566,7 +557,6 @@
         <dependency>
           <groupId>io.netty</groupId>
           <artifactId>netty-transport-native-epoll</artifactId>
-          <version>${io.netty.version}</version>
           <classifier>${io.netty.netty-transport-native-epoll.classifier}</classifier>
           <scope>${io.netty.netty-transport-native-epoll.scope}</scope>
         </dependency>

diff --git a/schema/openapi.yaml b/schema/openapi.yaml
@@ -85,6 +85,7 @@ components:
     DiscoveryPlugin:
       properties:
         builtin:
+          readOnly: true
           type: boolean
         callback:
           format: uri
@@ -296,6 +297,7 @@ components:
     Target:
       properties:
         agent:
+          readOnly: true
           type: boolean
         alias:
           pattern: \S
@@ -347,11 +349,6 @@ components:
         meta:
           $ref: '#/components/schemas/Meta'
       type: object
-  securitySchemes:
-    SecurityScheme:
-      description: Authentication
-      scheme: basic
-      type: http
 info:
   contact:
     email: [email protected]
@@ -913,7 +910,7 @@ paths:
             type: string
       requestBody:
         content:
-          application/json:
+          text/plain:
             schema:
               type: string
       responses:
@@ -1906,7 +1903,7 @@ paths:
       responses:
         "200":
           content:
-            application/json:
+            text/plain:
               schema:
                 type: string
           description: OK
@@ -2393,13 +2390,13 @@ paths:
             type: integer
       requestBody:
         content:
-          application/json:
+          text/plain:
             schema:
               type: string
       responses:
         "200":
           content:
-            application/json:
+            text/plain:
               schema:
                 type: string
           description: OK
@@ -2429,7 +2426,7 @@ paths:
       responses:
         "200":
           content:
-            application/json:
+            text/plain:
               schema:
                 type: string
           description: OK

diff --git a/src/main/java/io/cryostat/HibernateFormatMapperCustomization.java b/src/main/java/io/cryostat/HibernateFormatMapperCustomization.java
@@ -0,0 +1,46 @@
+/*
+ * Copyright The Cryostat Authors.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package io.cryostat;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import io.quarkus.hibernate.orm.JsonFormat;
+import io.quarkus.hibernate.orm.PersistenceUnitExtension;
+import org.hibernate.type.descriptor.WrapperOptions;
+import org.hibernate.type.descriptor.java.JavaType;
+import org.hibernate.type.format.FormatMapper;
+import org.hibernate.type.format.jackson.JacksonJsonFormatMapper;
+
+@JsonFormat
+@PersistenceUnitExtension
+/**
+ * @see https://github.com/quarkusio/quarkus/issues/42596
+ */
+public class HibernateFormatMapperCustomization implements FormatMapper {
+
+    private final JacksonJsonFormatMapper delegate =
+            new JacksonJsonFormatMapper(new ObjectMapper().findAndRegisterModules());
+
+    @Override
+    public <T> T fromString(
+            CharSequence charSequence, JavaType<T> javaType, WrapperOptions wrapperOptions) {
+        return delegate.fromString(charSequence, javaType, wrapperOptions);
+    }
+
+    @Override
+    public <T> String toString(T value, JavaType<T> javaType, WrapperOptions wrapperOptions) {
+        return delegate.toString(value, javaType, wrapperOptions);
+    }
+}
diff --git a/src/main/java/io/cryostat/credentials/Credentials.java b/src/main/java/io/cryostat/credentials/Credentials.java
@@ -25,7 +25,6 @@
 import io.cryostat.expressions.MatchExpression;
 import io.cryostat.expressions.MatchExpression.TargetMatcher;
 
-import io.smallrye.common.annotation.Blocking;
 import jakarta.annotation.security.RolesAllowed;
 import jakarta.inject.Inject;
 import jakarta.transaction.Transactional;
@@ -113,7 +112,6 @@ static Map<String, Object> notificationResult(Credential credential) throws Scri
         return result;
     }
 
-    @Blocking
     static Map<String, Object> safeResult(Credential credential, TargetMatcher matcher)
             throws ScriptException {
         Map<String, Object> result = new HashMap<>();
@@ -124,7 +122,6 @@ static Map<String, Object> safeResult(Credential credential, TargetMatcher match
         return result;
     }
 
-    @Blocking
     static Map<String, Object> safeMatchedResult(Credential credential, TargetMatcher matcher)
             throws ScriptException {
         Map<String, Object> result = new HashMap<>();

diff --git a/src/main/java/io/cryostat/credentials/CredentialsFinder.java b/src/main/java/io/cryostat/credentials/CredentialsFinder.java
@@ -24,7 +24,6 @@
 import io.cryostat.targets.Target.TargetDiscovery;
 
 import io.quarkus.vertx.ConsumeEvent;
-import io.smallrye.common.annotation.Blocking;
 import jakarta.enterprise.context.ApplicationScoped;
 import jakarta.inject.Inject;
 import org.apache.commons.collections4.BidiMap;
@@ -52,7 +51,6 @@ void onMessage(TargetDiscovery event) {
         }
     }
 
-    @Blocking
     public Optional<Credential> getCredentialsForTarget(Target target) {
         return Optional.ofNullable(
                 cache.computeIfAbsent(
@@ -73,7 +71,6 @@ public Optional<Credential> getCredentialsForTarget(Target target) {
                                         .orElse(null)));
     }
 
-    @Blocking
     public Optional<Credential> getCredentialsForConnectUrl(URI connectUrl) {
         return Target.find("connectUrl", connectUrl)
                 .<Target>singleResultOptional()

diff --git a/src/main/java/io/cryostat/discovery/ContainerDiscovery.java b/src/main/java/io/cryostat/discovery/ContainerDiscovery.java
@@ -187,7 +187,6 @@ public abstract class ContainerDiscovery {
 
     protected long timerId;
 
-    @Transactional
     void onStart(@Observes StartupEvent evt) {
         if (!enabled()) {
             return;
@@ -201,7 +200,6 @@ void onStart(@Observes StartupEvent evt) {
         }
 
         logger.debugv("Starting {0} client", getRealm());
-
         queryContainers();
         this.timerId = vertx.setPeriodic(pollPeriod.toMillis(), unused -> queryContainers());
     }
@@ -266,10 +264,9 @@ private Target toTarget(ContainerSpec desc) {
         target.connectUrl = connectUrl;
         target.alias = Optional.ofNullable(desc.Names.get(0)).orElse(desc.Id);
         target.labels = desc.Labels;
-        target.annotations = new Annotations();
-        target.annotations
-                .cryostat()
-                .putAll(
+        target.annotations =
+                new Annotations(
+                        null,
                         Map.of(
                                 "REALM", // AnnotationKey.REALM,
                                 getRealm(),

diff --git a/src/main/java/io/cryostat/discovery/CustomDiscovery.java b/src/main/java/io/cryostat/discovery/CustomDiscovery.java
@@ -200,9 +200,7 @@ Response doV2Create(
             credential.ifPresent(c -> c.persist());
 
             target.activeRecordings = new ArrayList<>();
-            target.labels = Map.of();
-            target.annotations = new Annotations();
-            target.annotations.cryostat().putAll(Map.of("REALM", REALM));
+            target.annotations = new Annotations(null, Map.of("REALM", REALM));
 
             DiscoveryNode node = DiscoveryNode.target(target, BaseNodeType.JVM);
             target.discoveryNode = node;